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The Sudetenland, located on the Czechoslovak border with Germany and Austria proper, with its majority of ethnic German inhabitants, had been incorporated directly into the Reich on October 10, 1938, when Czechoslovakia was forced to accept the terms of the Munich Agreement. Five months later, when the Slovak Diet declared the independence of Slovakia, Hitler summoned Czechoslovak President Emil Hácha to Berlin and intimidated him into accepting the German occupation of the Czech rump state.

Bohemia and Moravia were declared a protectorate of Germany and were placed under the supervision of the Reichsprotektor, Konstantin von Neurath. Hácha remained as technical head of state with the title of State President; German officials manned departments analogous to cabinet ministries, while small German control offices were established locally. The Gestapo assumed police authority. Jews were dismissed from the civil service and placed in an extralegal position. Political parties were banned, and many Communist Party leaders fled to the Soviet Union.

The population of the protectorate was mobilized for labor that would aid the German war effort, and special offices were organized to supervise the management of industries important to that effort. Czechs were drafted to work in coal mines, the iron and steel industry, and armaments production; some young people were sent to Germany. Consumer goods production, much diminished, was largely directed toward supplying the German armed forces. The protectorate's population was subjected to strict rationing.

German rule was moderate during the first months of the occupation. The Czech government and political system, reorganized by Hácha, continued in formal existence. Gestapo activities were directed mainly against Czech politicians and the intelligentsia. Nevertheless, the Czechs demonstrated against the occupation on October 28, 1939 the anniversary of Czechoslovak independence. The death on November 15, 1939 of a medical student, Jan Opletal, who had been wounded in the October violence, precipitated widespread student demonstrations, and the Reich retaliated. Politicians were arrested en masse, as were an estimated 1,800 students and teachers. On November 17, all universities and colleges in the protectorate were closed, nine student leaders were executed, and hundreds were sent to concentration camps in Germany. (See also Czech resistance to Nazi occupation)

During World War II, on September 27, 1941, the Reich adopted a more radical policy in the protectorate. SS-hardliner Reinhard Heydrich was appointed Deputy Reichsprotektor of Bohemia and Moravia. Under his authority Prime Minister Alois Eliáš was arrested (and later executed), the Czech government was reorganized, and all Czech cultural organizations were closed. The Gestapo indulged in arrests and executions. The deportation of Jews to concentration camps was organized, and the fortress town of Terezín was made into a ghetto way station for Jewish families. On June 4, 1942, Heydrich died after being wounded by an assassin in Operation Anthropoid. Heydrich's successor, Colonel General Kurt Daluege, ordered mass arrests and executions and the destruction of the villages of Lidice and Ležáky. In 1943 the German war effort was accelerated. Under the authority of Karl Hermann Frank, German minister of state for Bohemia and Moravia, some 350,000 Czech laborers were dispatched to the Reich. Within the protectorate, all non-war-related industry was prohibited. Most of the Czech population obeyed quiescently up until the final months preceding the end of the war, while thousands were involved in the resistance movement.

For the Czechs of the Protectorate Bohemia and Moravia, German occupation was a period of brutal oppression, made even more painful by the memory of independence and democracy.

Czech losses resulting from political persecution and deaths in concentration camps totaled between 36,000 and 55,000.
The Jewish population of Bohemia and Moravia (118,000 according to the 1930 census) was virtually annihilated. Many Jews emigrated after 1939; more than 70,000 were killed; 8,000 survived at Terezín. Several thousand Jews managed to live in freedom or in hiding throughout the occupation.
The extermination of the Romani population was so thorough that the Bohemian Romani language became totally extinct. Romani internees were sent to the Lety and Hodonín concentration camps before being transferred to Auschwitz-Birkenau for gassing. The vast majority of Romani in the Czech Republic today are actually descended from migrants from Slovakia who moved there during the post-war years in Czechoslovakia.

For administrative purposes, the Protectorate of Bohemia and Moravia was divided into two Lands; Böhmen (Bohemia) and Mähren (Moravia). Each of these was further subdivided into Oberlandratsbezirke, each comprising a number of Bezirke.